NGUI doesn't work correctly from asset bundles. It never had, and I'm surprised you didn't run into such issues before. I'm guessing its related to a global list of draw calls. I plan on changing it back to where each panel owning their own draw calls in the near future, so it should address this issue as well.
However as I said... asset bundles + NGUI is not a good combination.
I get some weird "Fatal Error! CheckDisalowAllocation. Allocating memory when it is not allowed to allocate memory." error at random if I open up a scene with ngui, make some changes like rename some text in a label, and when i go to load another scene after saving the current scene it crashes with that error.
I have the same problem (in my case running Unity 4.2.2). And also I see this in console sometimes:
"Destroying object multiple times. Don't use DestroyImmediate on the same object in OnDisable or OnDestroy."
It has to be NGUI because I don't use anywhere DestroyImmediate in my project and I don't have any other assets.
I know it's something between 3.0.3 and 3.0.7... Please Aren take a look because it crashes Unity!!